Naruto: Petals of Time
by Yuki Kyuu Aizawa
Summary: It's been a thousand years since the fourth great ninja war. Much has changed. the Hiding Ninja villages are destroyed, from there ashes are kingdoms. With war on the horizon, two heroes must rise up. Some Yaoi.
1. Introduction: Fear of him

So hey there guys. Here's my new fanfiction. This ones going to be really hard to write. There will be Yaoi, but it won't be that important to the story. Well not much. Everything will be explained in Chapter One: Time, and ruins.

Disclaimer: I don't own Naruto, and any of the characters, moves, locations, etc. All rights go to their respected owners.

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_'Run, come on, run!' _The thought races through my mind. I run silently through a forest. My lungs are screaming for air, but I ignore them. If I stop now, they would catch up to me. My sweat is coating my body, and I have a cut on my cheek. I only have to escape from them. I soon run out into a clearing, and immediately stop. Standing in front of me is a man with raven black hair like mine. His eyes dimly glow a blood red. He wore black ANBU pants, and a black long sleeve shirt. He has a mask that's familiar. Through the mask I can see the dim blood red glow of his eyes. Fear rushes through me. "Where do you think your going?" The man asked. HIs voice was deep, and sounded like death was talking. His hand gripped a foreign long sword. I couldn't help it. I began to shake in fear.

This man was the only person who was ever able to paralyze me with fear. "Do you really think you can escape from us? You're more foolish then I thought little brother." He took a step forward, and I took a step back. No, I can't let him capture me. I can't let him take me back. "What do you want Itachi?" I questioned. Itachi used to be my brother. I refuse to call him as such as now. He is nothing, but a tool. A weapon to be used against his enemies.

Itachi just stands there watching me. "You are a weapon just like me. We were created from two brothers DNA. You from the original Sasuke Uchiha's DNA, and me from Itachi Uchiha's DNA. We are weapons little brother. Along with Itachi's DNA, I was giving Madara Uchiha's DNA along with both their Shiringans." Itachi told me. Before I have time to react, Itachi rushes forward, and stabs me through the chest with his sword. The pain hurts so bad, I can't help but scream.


	2. Chapter 1: History repeats

So here is the first chapter I hope you guys like it. Please leave a review. This chapter is for background information.

Disclaimer: Read Introduction

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I awoke screaming. I shoot up from my bed. The sheets were drenched by sweat. I take a deep breath, and get out of bed. I still remember that day. I nearly died. I was saved by a being called Rune that appeared inside me. She is a black furred wolf, with red Shiringan eyes. She has ten tails, and on her back are raven wings. She healed me. Anyways I guess I should introduce myself I'm Sasuke Uchiha. No, not the avenger Sasuke. Perhaps I should explain.

Its been a thousand years since the end of The Fourth Great Ninja War. People call this the fourth era. Two years at the end of the war, two people went missing. One was Naruto Uzumaki, and the other was Sasuke Uchiha. People believe that Izanagi, and Izanami made them Kami. The church of Maki, says that Naruto the god that defends the world. They preach that Sasuke is the Demon God that wants to destroy the world. They control the Templars. This is a group made of Samurai, and Ninja that can use their own chakra to disrupt others. The church of Iha believes that both Sasuke and Naruto are lovers, much like Izanagi and Izanami themselves. I think that their dead. They have to be. Sure they were legends, and heroes, but they were only human.

For a hundred years after the war there was peace. Then something destroy the Hiding Ninja villages. Two years after, kingdoms arose from the ashes. They took the names of the villages, and grew. The major ones are Konoha, Rain, Cloud, Mist, Suna, Oto, and Fuyu. Konoha and Suna have an alliance along with Rain, Cloud, and Mist. Fuyu is neutral, and are trade allies with the other kingdoms. Oto is the remnant of Sound. Their leader is Yamato. Yamato is a tyrant, and the same as Orchimaru.

Thirty five years ago, Oto was approached by the remnants of the organization Akatski. They combined, forming the empire called Otkatski. Declaring war on Konoha, they began to take away land. The other kingdoms seeing this went to support Konoha. Otkatski began what they call the Uchiha Project. It was a project to replicate the Uchiha Ninjas, and enhance there strength. The first success was Itachi Uchiha. He was made using the DNA of the original Itachi, and also of Madara Uchiha. Desperate, Mist used what they could and were able to replicate the Ninja's Zabuza, and Haku. Suna replicated Gaara, Konkoha, and Temari. Fuyu were able to replicate the mysterious ninjas Yuki, Ice, Blizzard, and Fenirus. Konoha were able to replicate nearly all there ninja, including the fourth Hokage. The only one they couldn't replicate was Naruto Uzumaki. Fearing they would loose, Otkatski replicated the former Akatski members, and both Orchimaru and Kabuto. Two years later, the war ended with a treaty. It was that there would be no more research into replication. Some feared that the tailed beasts would be replicated, others that more then one replicated ninja would happen. I forgot to mention, but there can only be one replicated ninja of the original at a time. Otkatski however didn't listen. They continued with the Uchiha Project. Sixteen years ago I came into existence. I'm the second subject. A monster, a demon. Used as a weapon, a fucking tool by Otkatski. I was told I was replicated from the DNA of Sasuke Uchiha, and was used as the vessel of something. I was also able to use four Shiringans. The original Eternal Shirinagan, along with the Elemental Shiringan, Demon Shiringan, and Angel Shiringan. The Elemental allows me to use all elemental Justus, even bloodline Justus.

I'm traveling to the ruins of the Hiding leaf village. Something is drawing me to there. I can't help but feel like something will happen there. For three years I've been on the run. I just want peace. The ruins are a day away on foot, but using chakra to jump from tree to tree, it would be easy for me to get there in an hour. Silently I slip out of the room, and head to the edge of the town. I gather chakra in my feet, and take off. Inside me, Rune is thrashing against her cage. It causes me to wince.

It wasn't long before I stood in front of the gates. They were in ruins. I silently enter the village. As I walk, I can feel the tug of chakra. It's trying to call me. I walk to where its the strongest. It leads to an underground door. Red chakra is blocking me from opening it. I smile. Black chakra gathers around my hand, and I touch the red chakra. It dissipates, and I step inside. To my surprise there's a teenage boy sleeping on an alter. He's probably my age. His hair is a blond color that's like rays of sunlight. He has six whisker marks, three on each side of his face. When his eyes open I find they are a cerulean blue. There only one person with that eye color. "Sasuke?" _Oh shit._


	3. Chapter 2: Confused thoughts

Sorry it took me awhile to write this chapter. In truth I couldn't think of anything to write, that's how difficult writing this is. I just want to get it done though, so I hope you guys enjoy this. Please review.

Disclaimer: Read Introduction

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I started blankly at the blond. My mind was going on overdrive. It shouldn't be possible, it shouldn't be possible. I kept repeating it like a mantra. It's the truth. It shouldn't be possible. I knew who exactly it is. Its the most famous person, Naruto Uzumaki. He shouldn't even be alive. "Hey Sasuke you okay teme?" He asked. I blinked, and another memory goes through my mind. It was a memory that I don't even remember. When I come back to reality, Naruto was waving his hand back and forth in front of my face. "Hey teme you there?" He questioned. I jump back alert. "I'm not the Sasuke Uchiha that you know." I tell him. He looks at me, and then blinks in confusion.

I sigh, not really looking to explain about this at all. "Look, I'm a replicant. A clone of a Ninja's DNA. Specifically I was created using Sasuke's DNA." I tell him. He nods, and then sits down on the shrine. "So, how have you been able to make any money?" He asks. I look down at the ground. I've been trained to kill since I was created, so after I escaped, I took on a job as a Hunter Nin. It was really simple, and it helped me to avoid my brother. "A Hunter Nin." I state. Naruto's eyes went wide. I narrow my eyes at him. "What, it's not that big of a deal is it?" I ask. I'm not really sure.

Naruto shakes his head. "No, just that I'm surprised Ninjas still exist a thousand years into the future you know." He tells my. I nod my head. "So Sasuke, what happened to the hidden villages?" He questioned. I turned my head, not really wanting to answer him. "They were destroyed. A hundred years after the end of the Fourth Great Ninja War. I wanted to come here to escape, but instead I find you dope." I say. I'm irritated more then usual, but hey can you blame me. I wasn't expecting to find somebody who was suppose to be dead. It's really causing me to get a major headache.

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It wasn't that long before we left. We were heading back to the inn. I was trying to figure out someway to disguise Naruto, but nothing comes to him. The blond is unusually quiet. It was really starting to freak me out, though I didn't want to admit it. We took to the trees. Half way to the inn I had stayed at, we had to stop. It turns out that being a sleep for a thousand years really isn't that good for the bodies chakra system. Naruto was easily exhausted. I frowned. If he gets exhausted this easy, then that's really worrying. Even a thousand years after the Fourth Great Ninja War, the legends say that Naruto Uzumaki had nearly infinite chakra. It was also said that the original Sasuke Uchiha was able to rival the blond in power. So, I have a feeling that we were going to have to train. At least, if we want to be able to survive.

"Ne Sasuke?" The blond calls out my name. "Hn." He smiles slightly at that. "Where are we gong next?" He questioned. I've been thinking about that. I don't want to keep running from Otkatsuki forever, and so have been thing of a way to go against them. Right now though, I think we should head to the land of snow, or better called the Trade Republic of Fuyu, or to abbreviate T.R.F. They were neutral, and so it would be the best place for us to hide, without having to worry about any of Otkatsuki trackers. I'm not really scared of Otkatsuki. Only a few of the individual members freak me out. Those members are, Orchimaru, Kabuto, and Tobi/Obito. You might ask why I didn't add Itachi to that list. The answer is really simple. He doesn't freak me out, he makes me terrified. The blond is looking at me waiting for an answer.

"I was thinking we will head to the Trade Republic of Fuyu." He tilts his head to the side. I mentally face palm. I forgot that Naruto doesn't know any of the newer country names. "Its in the land of snow. Most of the Ninjas there have a high connection to water, and are able to manipulate the snow. It will be the best place to hide from my brother until I can come up with a better plan." I say. Naruto only nods and goes back to contemplating. Finally he got up, and looked at Sasuke. "Lets get going, I'm tiered, and would like to sleep on a real bed." He said. I nod, and get up to follow him. We take off into the trees again. It's not long before we come to the inn I had stayed at. It was a traditional Konoha inn, which means that it resembles a normal Japanese inn. The inn keeper was a female, maybe around the age of seventy. Her hair was an ash grey color, and her eyes were a dull violet. She must have been pretty when she was young. "One room, with a double bed?" She asks when she sees us. I blush. The old woman thought that Naruto and I were a couple. I was momentarily to shocked to answer, but Naruto did it for me.

"Yes, thank you. We will be leaving tomorrow." He said. The old woman nodded, and I glared at the stupid dope. Wait, were did I get that from anyways? It just felt right calling the dope a dope. Kami, there I go again. I sigh, and head to the room. Naruto stares at my back, and then begins to follow me. I quickly take off my shirt, leaving me in my pants. I can feel the blonds eyes on me, and they make me feel slightly insecure. I don't like people looking at what I have on my back. I've always had it.

"So, did you get a tattoo?" He questions. I shake my head, and bite my lower lip. I didn't want to tell him that I've always had it. It came with having rune sealed inside me. He lightly traced the markings. The markings were designed to look like a pair of black wings that rested on my back. I gasp when he traces the ones that connect my tail bone. They were designed to look like a wolf tail. Rune has told me that the more I relied on her power, the more wolf tails that would manifest. In all truth in honesty, it made me nervous. I turn to look at the blond. He seems to be enthralled by my markings. I start to moan. They were highly sensitive. Naruto quickly draws his hand back, and smiles sheepishly. I turn so he doesn't see the blush, and pout I have on my face. Finally, I'm able to compose my face, and I stare back at him. "Come on Uzumaki-san, lets get to sleep." I say. He scowls when I call him that. "Just call me Naruto." He says. I stare at him dumbfounded. I blink once, then twice. I then let a small smirk come across my face. "Okay Na~ru~to." I say. I watch with amusement as Naruto blushes slightly. I find it quiet amusing if you know why. We both get into the bed. I'm still ticked that the old lady thought we were a couple, but now that I think about it. I wouldn't mind if Naruto and me were. Rune seems to be communicating to Kurama. Yes, Rune has told me about Naruto's Tailed Beast. I wonder what's Runes old relationship was too Kurama. The way she talked about him it was almost as if they were-." I quickly shut that part of my mind down. Silently I drift off, all my thoughts on a certain blond individual, and what are next move would be.

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At the capitol of the Empire of Otkatsuki

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Itachi stood in front of Yamato. He sighed. He had taken over the throne of Otkatsuki easily. The military was willing to follow him. Now he had to think of a way to show that he will not accept rebellion. A smile forms on his lips. He order Kabuto to come in. "Perform some experiments on him, when he's dead replicate him. I'm sure you know where I'm going with this." He stated. Kabuto nodded. Yamato screamed, as he was dragged out of the throne room. He sat on the throne, and was deep in thought.

_'Where are you little brother?'_ He questioned in his mind. It was like Sasuke dropped off the map completely. He had no idea, where he went. Itachi would never admit it, but he worried for his little brother, but because of his genes he couldn't care. Sasuke was a problem that had too be taken care of. If he came into contact with the container of the Nine Tails, then all his memories would return. Everything that he forgot after that infernal ten-tails was sealed in him. The last he had gotten word, was that he was traveling to the ruins of Konoha. Itachi sighed.

Later today, he would have to meet with delegeates from other nations. He would tell them that he was the new Emperor. He was already thinking of repelcating the Uchiha. The Sharingan would be the new flag of the Otkatsuki, and it would be surrounded by four red clouds, and then two musical symbols. Yes, Otkatsuki would be the ruler of the world. He wouldn't let the other nations know just yet.

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Okay, so that's the end of the second chapter. Hope you enjoyed it. Please review, and get others to read this.


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